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Saturday, August 6, 2016

Yamnaya dogs (?)

Just in at bioRxiv:

Abstract: Europe has played a major role in dog evolution, harbouring the oldest uncontested Palaeolithic remains and having been the centre of modern dog breed creation. We sequenced the whole genomes of an Early and End Neolithic dog from Germany, including a sample associated with one of Europe’s earliest farming communities. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a Late Neolithic population replacement previously suggested by analysis of mitochondrial DNA and a Late Neolithic Irish genome. However, our End Neolithic sample possesses additional ancestry found in modern Indian dogs, which we speculate may be derived from dogs that accompanied humans from the Eastern European steppe migrating into Central Europe. By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000-40,000 years ago. Interestingly, the extreme copy number expansion of the AMY2B gene found in modern dogs was not observed in the ancient samples, indicating that the AMY2B copy number increase arose as an adaptation to starch-rich diets after the advent of agriculture in the Neolithic period.

And on page 17:

The age of the samples provide a time frame, between ~7,000 and 5,000 years ago, for CTC to obtain its additional Indian­like ancestry component. Considering that CTC shows similar admixture patterns to Central Asian and Middle Eastern modern dog populations, as seen in the PCA (Figure 2) and ADMIXTURE (Supplementary Figure S8.3.2.) analysis, and that the cranium was found next to two individuals associated with the Neolithic Corded Ware Culture, we speculate that the Indian­-like gene flow may have been acquired by admixture with incoming populations of dogs that accompanied steppe people migrating from the East. Moreover, ADMIXTUREGRAPH and ​ f4 statistics support the possibility that the Indian and the wolf ancestry are the consequence of the same admixture event, involving a dog population that carried the two ancestries. This scenario is further supported by the model estimated by G­PhoCS, which infers substantial migration from wolves to the lineage represented by Indian village dogs (and as much as 0.36 migration rate when Indian wolves are included in the tree (Supplementary Methods 12)).

However, SpaceMix additionally inferred around 10% ancestry in CTC (but not HXH or NGD) from the geogenetic space containing Old World wolves (Supplementary Figure S8.2.3). ​f4 statistics of the form ​f4(CTC,HXH,Wolf,Outgroup) suggest that the likely origin of this wolf component is related to contemporary Iranian/Indian wolves (those with the least amount of dog admixture, as revealed using an ​f4­ratio test and SpaceMix, Supplementary Methods 10).

Someone could also argue that Bronze Age steppe wolves migrated to Iran and India following the Indo-Europeans.

@ all,See. its always possible to put a spin when is in our interest (pet theory). I love it. ;)

Here, at eurogenes we always follow the DNA...up until it contradicts us! Paper is clear. There were neolithic dogs and then there was the arrival of the CWC with dogs with a considerable amount of India dogs DNA. So... hum, those R1a guys carried dogs that and Indian ancestry? wasn't there something called Out of India regarding R1a?

@bellbeakerblogger,You probably don't remember, but I was the guy way back when that only wanted to talk about Grapes, Horses and.... Dogs. Remember.That was prior to me writing my thesis regarding Shulaveri 2 bell beakers.

to the topic: There is also Mtdna dog haplogroup D. And the only dogs that belong to that haplogroup are the KANGAL Dog (ancestral isolated Eastern Anatolia!) pretty near the Caucasus, the Portuguese SERRA DA ESTRELA (ancestral isolated Portugeses dog) and the SPANISH GALGO.The spanish Galgo is thought to be the Greyhound dog that was depicted in Ancient Egypt pictures and in the Tibesti paintings of the Tassili Mountains as the Bovidean pastoral II (white man phase).

Funny, I wrote the thesis but never did the chapters I wanted to make from the start regarding Grapes, Horses and Dogs.... those chapters are still blank in my website (http://shulaveri2bellbeaker.blogs.sapo.pt/)

A caveat is the following:"We therefore utilize call set 3, with variants ascertained in New World wolves, as the primary call set for most analyses.""We note that gene flow between New World wolves and Old World canids could potentially bias the observed genetic variation in this call set. However, previous genomic studies have reported very low to negligible migration rates only between Mexican wolves and Basenji/Dingo ​(Fan et al. 2016)and analysis of one locus under positive selection that confers black coat color suggests a potential old introgression from dogs to North American wolves (though we note that selection on standing variation cannot be ruled out) ​(Anderson et al. 2009) ​. In both cases these admixture events should have minimal impact on our analyses which primarily involve Eurasian dogs."They seem to have overlooked Ding e.a. (2012) (missing from their literature list) that demonstrated yDNA 6, prevalent in N/C China, having undergone admixture with N. American wolves (suggesting back-migration Out of America suring the mid-holocene).http://www.nature.com/hdy/journal/v108/n5/full/hdy2011114a.html

I don't know how that ascertainment bias affects their overall conclusions related to the tree phylogeny and Asian admixture. However, as in all papers I have read so far, inferred split times are too late to explain the occurrence of domesticated dogs in the Fanco-Iberian Magdalenian 18-15 ky ago by "import" from South/East Asia.https://www.animalsciencepublications.org/publications/af/pdfs/4/3/23 https://paleo.revues.org/2465

An interesting speculation is whether the Indian signal in CTC actually stems from the Zagros, which has early evidence of dog domestication (Pelagwa, ca. 12.000 BC). Of course, if you are into goat- and shepherding, dogs come in handy. The Gobustan petroglyphs have dogs appearing in Neolithic / Chalcolithic contexts, they obviously spread to the Caspian together with pastoralism.As such, it may also be envisaged that the difference between HXH and CTC relates to different purposes of the dogs in question.

"CTC was an adult dog​ demonstrating morphological similarity to the so­called Torfhund (​Canis familiaris palustris)"The Torfhund has been first described for LN Swiss pile dwellings, but ist oldest find was made in a LBK settlement context (Zschernitz, Saxony). It is assumed to have looked similar to the Wolfsspitz/ Keeshound, a traditional watchdog with little hunting instinct.

Addendum on the "Torfhund": The first description relates to La Neuveville-Schafis on the Lake of Bienne/Biel. The settlement has been dendrodated to the 32/31st cent. BC, and belongs to the Lattrigen complex, a Western Swiss variant of the Horgen Culture. As such, appearance of the "Torfhund" predates CWC/Yamnaya. Note also that W. Switzerland was never in earnest reached by CWC. Instead, the local early 4th. mBC Auvernier Culture shows continuity with the preceding Lattrigen and Lüscherz complexes, and influence from the neolithique finale of the French Jura and the Saone plain.

Ryukendo, Indeed this is only one dog sample and it would be unwise to make sweeping arguments for human movement based on it.

The East Asian introgression into European Neolithic dogs is independent and earlier to the Indian dog introgression. It perhaps dates to the period when an East Asian genetic input occurred in European HG groups.

The comments on this post are so fantastic. It is really great to hear the wisdom.

So from what I have heard, we still have very little knowledge of where and when major dog admixture events occured. We don't know when and where they were domesticated. We don't know when or where admixture with 'wild' polulations of either wolves, or feral dogs, or hybrids occured.

Lots of space for future genomic studies.

So, after reading most if the related literature, it apoears I was wrong in my earlier comment.

Not even close to being enough data, or acurate models of how domesticated species interact with humans and feral and/or wild populations.

At least there's enough data to say the dogs of southern East Asia are the most basal ones, their position relative to other dogs in phylogenic trees (or TreeMix) rooted in various canids is similar to that of SSA relative to Eurasians in human trees. TreeMix with edges indicates this is not a product of admixture from wolves either.

"At least there's enough data to say the dogs of southern East Asia are the most basal ones"

There is enough data to say that the modern dogs of southern East Asia have the largest amounts of 'dog' diversity (excluding non-dog modern wolves).

However, we still know very little about extinct wolf variation across Eurasia. The data we do have is suggestive that all modern grey wolves arose from a severe bottleneck. This leaves a lot of area and time for dogs to have been domesticated almost anywhere in Eurasia (but obviously long before ~15,000 years ago, when fully domesticated dogs entered the Americas).

I don't think extinct wolves matter all that much. We don't see migration edges from roots of wolf branches or from between dogs and wolves or wolves and coyotes to significant dog populations (dingos and NG singing dogs may have some). Something like modern Middle Eastern wolves admixed into African village dogs and Basenji.

Of course. And we don't see Neanderthal admixture edges into SSA humans.

By extinct wolves, I mean entire extinct lineages. Not something more related to existing wolves than existing dogs. In fact, they should be more related to existing dogs, and you could only see them as a ghost population.

no idea on the dog question except it made me wonder - if you had multiple regional breeds of dog among various categories: hunting dogs, sheep dogs etc then the best one in a particular category may have won i.e. the best sheep herding dog breed at the time displaced all the others.

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off topic random thought of the day - i wonder how much more force you need to get a stone spear through a mammoth's hide (fur/hair?) than a deer's? my guess is quite a lot more. if that was so then the guy holding / throwing the spear would probably need to be bigger / stronger than a deer hunter.